Mercurial > repos > iuc > bedtools
diff shuffleBed.xml @ 17:44867b59dbf2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
author | iuc |
---|---|
date | Tue, 05 Sep 2017 15:40:14 -0400 |
parents | 7308cc546a36 |
children | a8eabd2838f6 |
line wrap: on
line diff
--- a/shuffleBed.xml Fri Aug 18 15:33:08 2017 -0400 +++ b/shuffleBed.xml Tue Sep 05 15:40:14 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0"> +<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.1"> <description>randomly redistrubute intervals in a genome</description> <macros> <import>macros.xml</import> @@ -8,7 +8,7 @@ <command> <![CDATA[ bedtools shuffle - -g '$genome' + -g @GENOME_FILE@ -i '$inputA' $bedpe #if str($seed.seed_choose) == "True": @@ -31,7 +31,7 @@ <inputs> <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> - <expand macro="genome" /> + <expand macro="input_conditional_genome_file" /> <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue="" label="Keep features in the input file on the same chromosome" help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" /> @@ -67,6 +67,7 @@ <tests> <test> <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> + <param name="genome_file_opts_selector" value="hist" /> <param name="genome" value="shuffleBed.len" ftype="tabular" /> <param name="chrom" value="" /> <param name="seed_choose" value="True" /> @@ -75,6 +76,7 @@ </test> <test> <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> + <param name="genome_file_opts_selector" value="hist" /> <param name="genome" value="shuffleBed.len" ftype="tabular" /> <param name="chrom" value="True" /> <param name="seed_choose" value="True" /> @@ -83,6 +85,7 @@ </test> <test> <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> + <param name="genome_file_opts_selector" value="hist" /> <param name="genome" value="shuffleBed.len" ftype="tabular" /> <param name="excl" value="shuffleBed2.bed" ftype="bed" /> <param name="seed_choose" value="True" /> @@ -91,6 +94,7 @@ </test> <test> <param name="inputA" value="shuffleBed1.bed" ftype="bed" /> + <param name="genome_file_opts_selector" value="hist" /> <param name="genome" value="shuffleBed.len" ftype="bed" /> <param name="allow_beyond" value="True" /> <param name="seed_choose" value="True" />